메뉴 건너뛰기




Volumn 79, Issue 7, 2011, Pages 2327-2334

The ygeW encoded protein from Escherichia coli is a knotted ancestral catabolic transcarbamylase

Author keywords

Knotted protein; Purine degradation pathway; Transcarbamylase; ygeW gene

Indexed keywords

BACTERIAL PROTEIN; CARBAMOYLTRANSFERASE; PROTEIN YGEW; UNCLASSIFIED DRUG;

EID: 79958770988     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23043     Document Type: Article
Times cited : (15)

References (57)
  • 1
    • 0017122896 scopus 로고
    • Degradation of purines and pyrimidines by microorganisms
    • Vogels GD, Van der Drift C. Degradation of purines and pyrimidines by microorganisms. Bacteriol Rev 1976; 40: 403-468.
    • (1976) Bacteriol Rev , vol.40 , pp. 403-468
    • Vogels, G.D.1    Van der Drift, C.2
  • 2
    • 0014034942 scopus 로고
    • Epidemiology of gout and hyperuricemia. A long-term population study
    • Hall AP, Barry PE, Dawber TR, McNamara PM. Epidemiology of gout and hyperuricemia. A long-term population study. Am J Med 1967; 42: 27-37.
    • (1967) Am J Med , vol.42 , pp. 27-37
    • Hall, A.P.1    Barry, P.E.2    Dawber, T.R.3    McNamara, P.M.4
  • 3
    • 0019787519 scopus 로고
    • Uric acid provides an antioxidant defense in humans against oxidant- and radical-caused aging and cancer: a hypothesis
    • Ames BN, Cathcart R, Schwiers E, Hochstein P. Uric acid provides an antioxidant defense in humans against oxidant- and radical-caused aging and cancer: a hypothesis. Proc Natl Acad Sci USA 1981; 78: 6858-6862.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 6858-6862
    • Ames, B.N.1    Cathcart, R.2    Schwiers, E.3    Hochstein, P.4
  • 4
    • 3042692195 scopus 로고    scopus 로고
    • Isolation of a chromosomal region of Klebsiella pneumoniae associated with allantoin metabolism and liver infection
    • Chou HC, Lee CZ, Ma LC, Fang CT, Chang SC, Wang JT. Isolation of a chromosomal region of Klebsiella pneumoniae associated with allantoin metabolism and liver infection. Infect Immun 2004; 72: 3783-3792.
    • (2004) Infect Immun , vol.72 , pp. 3783-3792
    • Chou, H.C.1    Lee, C.Z.2    Ma, L.C.3    Fang, C.T.4    Chang, S.C.5    Wang, J.T.6
  • 5
    • 33646580070 scopus 로고    scopus 로고
    • Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes
    • Ramazzina I, Folli C, Secchi A, Berni R, Percudani R. Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes. Nat Chem Biol 2006; 2: 144-148.
    • (2006) Nat Chem Biol , vol.2 , pp. 144-148
    • Ramazzina, I.1    Folli, C.2    Secchi, A.3    Berni, R.4    Percudani, R.5
  • 6
    • 4644275038 scopus 로고    scopus 로고
    • Serum uric acid-lowering therapies: where are we heading in management of hyperuricemia and the potential role of uricase
    • Bomalaski JS, Clark MA. Serum uric acid-lowering therapies: where are we heading in management of hyperuricemia and the potential role of uricase. Curr Rheumatol Rep 2004; 6: 240-247.
    • (2004) Curr Rheumatol Rep , vol.6 , pp. 240-247
    • Bomalaski, J.S.1    Clark, M.A.2
  • 7
    • 77950398327 scopus 로고    scopus 로고
    • Ureide catabolism in Arabidopsis thaliana and Escherichia coli
    • Werner AK, Romeis T, Witte CP. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nature Chem Biol 2010; 6: 19-21.
    • (2010) Nature Chem Biol , vol.6 , pp. 19-21
    • Werner, A.K.1    Romeis, T.2    Witte, C.P.3
  • 8
    • 0009823739 scopus 로고
    • Streptococcus allantoicus and the fermentation of allantoin
    • Barker HA. Streptococcus allantoicus and the fermentation of allantoin. J Bacteriol 1943; 46: 251-259.
    • (1943) J Bacteriol , vol.46 , pp. 251-259
    • Barker, H.A.1
  • 10
    • 0344879063 scopus 로고
    • Induction of carbamyl-P specific oxamate transcarbamylase by parabanic acid in a Streptococcus
    • Tigier H, Grisolia S. Induction of carbamyl-P specific oxamate transcarbamylase by parabanic acid in a Streptococcus. Biochem Biophys Res Commun 1965; 19: 209-214.
    • (1965) Biochem Biophys Res Commun , vol.19 , pp. 209-214
    • Tigier, H.1    Grisolia, S.2
  • 12
  • 14
    • 36949064964 scopus 로고
    • Phosphate-dependent degradation of urea
    • Valentine RC, Wolfe RS. Phosphate-dependent degradation of urea. Nature 1961; 191: 925-926.
    • (1961) Nature , vol.191 , pp. 925-926
    • Valentine, R.C.1    Wolfe, R.S.2
  • 15
    • 0033797245 scopus 로고    scopus 로고
    • Purine catabolism in Escherichia coli and function of xanthine dehydrogenase in purine salvage
    • Xi H, Schneider BL, Reitzer L. Purine catabolism in Escherichia coli and function of xanthine dehydrogenase in purine salvage. J Bacteriol 2000; 182: 5332-5341.
    • (2000) J Bacteriol , vol.182 , pp. 5332-5341
    • Xi, H.1    Schneider, B.L.2    Reitzer, L.3
  • 16
    • 0032762639 scopus 로고    scopus 로고
    • Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli
    • Cusa E, Obradors N, Baldoma L, Badia J, Aguilar J. Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli. J Bacteriol 1999; 181: 7479-7484.
    • (1999) J Bacteriol , vol.181 , pp. 7479-7484
    • Cusa, E.1    Obradors, N.2    Baldoma, L.3    Badia, J.4    Aguilar, J.5
  • 17
    • 0036923450 scopus 로고    scopus 로고
    • Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS
    • Rintoul MR, Cusa E, Baldoma L, Badia J, Reitzer L, Aguilar J. Regulation of the Escherichia coli allantoin regulon: coordinated function of the repressor AllR and the activator AllS. J Mol Biol 2002; 324: 599-610.
    • (2002) J Mol Biol , vol.324 , pp. 599-610
    • Rintoul, M.R.1    Cusa, E.2    Baldoma, L.3    Badia, J.4    Reitzer, L.5    Aguilar, J.6
  • 18
    • 33646070547 scopus 로고    scopus 로고
    • Structural and biochemical study of effector molecule recognition by the E. coli glyoxylate and allantoin utilization regulatory protein AllR
    • Walker JR, Altamentova S, Ezersky A, Lorca G, Skarina T, Kudritska M, Ball LJ, Bochkarev A, Savchenko A. Structural and biochemical study of effector molecule recognition by the E. coli glyoxylate and allantoin utilization regulatory protein AllR. J Mol Biol 2006; 358: 810-828.
    • (2006) J Mol Biol , vol.358 , pp. 810-828
    • Walker, J.R.1    Altamentova, S.2    Ezersky, A.3    Lorca, G.4    Skarina, T.5    Kudritska, M.6    Ball, L.J.7    Bochkarev, A.8    Savchenko, A.9
  • 19
    • 33750267965 scopus 로고    scopus 로고
    • ORENZA: a web resource for studying ORphan ENZyme activities
    • Lespinet O, Labedan B. ORENZA: a web resource for studying ORphan ENZyme activities. BMC Bioinform 2006; 7: 436.
    • (2006) BMC Bioinform , vol.7 , pp. 436
    • Lespinet, O.1    Labedan, B.2
  • 20
    • 33746018654 scopus 로고    scopus 로고
    • Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis
    • Shi D, Morizono H, Cabrera-Luque J, Yu X, Roth L, Malamy MH, Allewell NM, Tuchman M. Structure and catalytic mechanism of a novel N-succinyl-L-ornithine transcarbamylase in arginine biosynthesis of Bacteroides fragilis. J Biol Chem 2006; 281: 20623-20631.
    • (2006) J Biol Chem , vol.281 , pp. 20623-20631
    • Shi, D.1    Morizono, H.2    Cabrera-Luque, J.3    Yu, X.4    Roth, L.5    Malamy, M.H.6    Allewell, N.M.7    Tuchman, M.8
  • 21
    • 34547611288 scopus 로고    scopus 로고
    • A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase
    • Shi D, Yu X, Cabrera-Luque J, Chen TY, Roth L, Morizono H, Allewell NM, Tuchman M. A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase. Protein Sci 2007; 16: 1689-1699.
    • (2007) Protein Sci , vol.16 , pp. 1689-1699
    • Shi, D.1    Yu, X.2    Cabrera-Luque, J.3    Chen, T.Y.4    Roth, L.5    Morizono, H.6    Allewell, N.M.7    Tuchman, M.8
  • 22
    • 33744491009 scopus 로고    scopus 로고
    • Expression, purification, crystallization and preliminary X-ray crystallographic studies of a novel acetylcitrulline deacetylase from Xanthomonas campestris
    • Shi D, Yu X, Roth L, Morizono H, Hathout Y, Allewell NM, Tuchman M. Expression, purification, crystallization and preliminary X-ray crystallographic studies of a novel acetylcitrulline deacetylase from Xanthomonas campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61: 676-679.
    • (2005) Acta Crystallogr Sect F Struct Biol Cryst Commun , vol.61 , pp. 676-679
    • Shi, D.1    Yu, X.2    Roth, L.3    Morizono, H.4    Hathout, Y.5    Allewell, N.M.6    Tuchman, M.7
  • 23
    • 0017184389 scopus 로고
    • A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding
    • Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 1976; 72: 248-254.
    • (1976) Anal Biochem , vol.72 , pp. 248-254
    • Bradford, M.M.1
  • 25
    • 0019799867 scopus 로고
    • An improved colorimetric assay for aspartate and ornithine transcarbamylases
    • Pastra-Landis SC, Foote J, Kantrowitz ER. An improved colorimetric assay for aspartate and ornithine transcarbamylases. Anal Biochem 1981; 118: 358-363.
    • (1981) Anal Biochem , vol.118 , pp. 358-363
    • Pastra-Landis, S.C.1    Foote, J.2    Kantrowitz, E.R.3
  • 26
    • 0031043291 scopus 로고    scopus 로고
    • Expression, purification and kinetic characterization of wild-type human ornithine transcarbamylase and a recurrent mutant that produces 'late onset' hyperammonaemia
    • Morizono H, Tuchman M, Rajagopal BS, McCann MT, Listrom CD, Yuan X, Venugopal D, Barany G, Allewell NM. Expression, purification and kinetic characterization of wild-type human ornithine transcarbamylase and a recurrent mutant that produces 'late onset' hyperammonaemia. Biochem J 1997; 322: 625-631.
    • (1997) Biochem J , vol.322 , pp. 625-631
    • Morizono, H.1    Tuchman, M.2    Rajagopal, B.S.3    McCann, M.T.4    Listrom, C.D.5    Yuan, X.6    Venugopal, D.7    Barany, G.8    Allewell, N.M.9
  • 27
    • 0032518449 scopus 로고    scopus 로고
    • Kinetic studies of allosteric catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa
    • Sainz G, Tricot C, Foray MF, Marion D, Dideberg O, Stalon V. Kinetic studies of allosteric catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa. Eur J Biochem 1998; 251: 528-533.
    • (1998) Eur J Biochem , vol.251 , pp. 528-533
    • Sainz, G.1    Tricot, C.2    Foray, M.F.3    Marion, D.4    Dideberg, O.5    Stalon, V.6
  • 28
    • 43749094344 scopus 로고    scopus 로고
    • The crystal structure of N-acetyl-L-glutamate synthase from Neisseria gonorrhoeae provides insights into mechanisms of catalysis and regulation
    • Shi D, Sagar V, Jin Z, Yu X, Caldovic L, Morizono H, Allewell NM, Tuchman M. The crystal structure of N-acetyl-L-glutamate synthase from Neisseria gonorrhoeae provides insights into mechanisms of catalysis and regulation. J Biol Chem 2008; 283: 7176-7184.
    • (2008) J Biol Chem , vol.283 , pp. 7176-7184
    • Shi, D.1    Sagar, V.2    Jin, Z.3    Yu, X.4    Caldovic, L.5    Morizono, H.6    Allewell, N.M.7    Tuchman, M.8
  • 30
    • 0035788107 scopus 로고    scopus 로고
    • Pushing the boundaries of molecular replacement with maximum likelihood
    • Read RJ. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr 2001; 57: 1373-1382.
    • (2001) Acta Crystallogr , vol.57 , pp. 1373-1382
    • Read, R.J.1
  • 32
    • 23844492576 scopus 로고    scopus 로고
    • Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment
    • Panjikar S, Parthasarathy V, Lamzin VS, Weiss MS, Tucker PA. Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment. Acta Crystallogr 2005; 61: 449-457.
    • (2005) Acta Crystallogr , vol.61 , pp. 449-457
    • Panjikar, S.1    Parthasarathy, V.2    Lamzin, V.S.3    Weiss, M.S.4    Tucker, P.A.5
  • 33
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallography
    • Collaborative Computational Project, Number 4
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr 1994; 50: 760-763.
    • (1994) Acta Crystallogr , vol.50 , pp. 760-763
  • 34
    • 37549039510 scopus 로고    scopus 로고
    • A short history of SHELX
    • Sheldrick GM. A short history of SHELX. Acta Crystallogr A 2008; 64: 112-122.
    • (2008) Acta Crystallogr A , vol.64 , pp. 112-122
    • Sheldrick, G.M.1
  • 35
    • 3442875865 scopus 로고    scopus 로고
    • ABS: a program to determine absolute configuration and evaluate anomalous scatterer substructure
    • Hao Q. ABS: a program to determine absolute configuration and evaluate anomalous scatterer substructure. J Appl Crystallogr 2004; 37: 498-499.
    • (2004) J Appl Crystallogr , vol.37 , pp. 498-499
    • Hao, Q.1
  • 37
    • 0032964481 scopus 로고    scopus 로고
    • Automated protein model building combined with iterative structure refinement
    • Perrakis A, Morris R, Lamzin VS. Automated protein model building combined with iterative structure refinement. Nat Struct Biol 1999; 6: 458-463.
    • (1999) Nat Struct Biol , vol.6 , pp. 458-463
    • Perrakis, A.1    Morris, R.2    Lamzin, V.S.3
  • 38
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr 2004; 60: 2126-2132.
    • (2004) Acta Crystallogr , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 40
  • 41
    • 0030802657 scopus 로고    scopus 로고
    • Crystal structure at 2.8 A resolution of anabolic ornithine transcarbamylase from Escherichia coli
    • Jin L, Seaton BA, Head JF. Crystal structure at 2.8 A resolution of anabolic ornithine transcarbamylase from Escherichia coli. Nat Struct Biol 1997; 4: 622-625.
    • (1997) Nat Struct Biol , vol.4 , pp. 622-625
    • Jin, L.1    Seaton, B.A.2    Head, J.F.3
  • 42
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr 2004; 60: 2256-2268.
    • (2004) Acta Crystallogr , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 43
  • 45
    • 0034710671 scopus 로고    scopus 로고
    • A deeply knotted protein structure and how it might fold
    • Taylor WR. A deeply knotted protein structure and how it might fold. Nature 2000; 406: 916-919.
    • (2000) Nature , vol.406 , pp. 916-919
    • Taylor, W.R.1
  • 46
    • 0037413604 scopus 로고    scopus 로고
    • Protein knots: a tangled problem
    • Taylor WR, Lin K. Protein knots: a tangled problem. Nature 2003; 421: 25.
    • (2003) Nature , vol.421 , pp. 25
    • Taylor, W.R.1    Lin, K.2
  • 47
    • 33749347406 scopus 로고    scopus 로고
    • Intricate knots in proteins: function and evolution
    • Virnau P, Mirny LA, Kardar M. Intricate knots in proteins: function and evolution. PLoS Comput Biol 2006; 2: e122.
    • (2006) PLoS Comput Biol , vol.2
    • Virnau, P.1    Mirny, L.A.2    Kardar, M.3
  • 48
    • 33646904782 scopus 로고    scopus 로고
    • Statistics of knots, geometry of conformations, and evolution of proteins
    • Lua RC, Grosberg AY. Statistics of knots, geometry of conformations, and evolution of proteins. PLoS Comput Biol 2006; 2: e45.
    • (2006) PLoS Comput Biol , vol.2
    • Lua, R.C.1    Grosberg, A.Y.2
  • 49
    • 78049235694 scopus 로고    scopus 로고
    • Knotted vs. unknotted proteins: evidence of knot-promoting loops
    • Potestio R, Micheletti C, Orland H. Knotted vs. unknotted proteins: evidence of knot-promoting loops. PLoS Comput Biol 2010; 6: e1000864.
    • (2010) PLoS Comput Biol , vol.6
    • Potestio, R.1    Micheletti, C.2    Orland, H.3
  • 50
    • 11044231848 scopus 로고    scopus 로고
    • The difficulty of annotating genes: the case of putrescine carbamoyltransferase
    • Naumoff DG, Xu Y, Stalon V, Glansdorff N, Labedan B. The difficulty of annotating genes: the case of putrescine carbamoyltransferase. Microbiology 2004; 150: 3908-3911.
    • (2004) Microbiology , vol.150 , pp. 3908-3911
    • Naumoff, D.G.1    Xu, Y.2    Stalon, V.3    Glansdorff, N.4    Labedan, B.5
  • 51
    • 9144265895 scopus 로고    scopus 로고
    • Retrieving sequences of enzymes experimentally characterized but erroneously annotated: the case of the putrescine carbamoyltransferase
    • Naumoff DG, Xu Y, Glansdorff N, Labedan B. Retrieving sequences of enzymes experimentally characterized but erroneously annotated: the case of the putrescine carbamoyltransferase. BMC Genomics 2004; 5: 52.
    • (2004) BMC Genomics , vol.5 , pp. 52
    • Naumoff, D.G.1    Xu, Y.2    Glansdorff, N.3    Labedan, B.4
  • 54
    • 1542286881 scopus 로고    scopus 로고
    • Analysis of an agmatine deiminase gene cluster in Streptococcus mutans UA159
    • Griswold AR, Chen YY, Burne RA. Analysis of an agmatine deiminase gene cluster in Streptococcus mutans UA159. J Bacteriol 2004; 186: 1902-1904.
    • (2004) J Bacteriol , vol.186 , pp. 1902-1904
    • Griswold, A.R.1    Chen, Y.Y.2    Burne, R.A.3
  • 55
    • 0035868405 scopus 로고    scopus 로고
    • Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes
    • Shi D, Morizono H, Yu X, Tong L, Allewell NM, Tuchman M. Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes. Biochem J 2001; 354: 501-509.
    • (2001) Biochem J , vol.354 , pp. 501-509
    • Shi, D.1    Morizono, H.2    Yu, X.3    Tong, L.4    Allewell, N.M.5    Tuchman, M.6
  • 56
    • 21144434991 scopus 로고    scopus 로고
    • Structural basis for ordered substrate binding and cooperativity in aspartate transcarbamoylase
    • Wang J, Stieglitz KA, Cardia JP, Kantrowitz ER. Structural basis for ordered substrate binding and cooperativity in aspartate transcarbamoylase. Proc Natl Acad Sci USA 2005; 102: 8881-8886.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 8881-8886
    • Wang, J.1    Stieglitz, K.A.2    Cardia, J.P.3    Kantrowitz, E.R.4
  • 57
    • 42449092465 scopus 로고    scopus 로고
    • Crystal structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase
    • Vitali J, Colaneri MJ, Kantrowitz E. Crystal structure of the catalytic trimer of Methanococcus jannaschii aspartate transcarbamoylase. Proteins 2008; 71: 1324-1334.
    • (2008) Proteins , vol.71 , pp. 1324-1334
    • Vitali, J.1    Colaneri, M.J.2    Kantrowitz, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.